FSL

FSL is a comprehensive library of analysis tools for FMRI, MRI and diffusion brain imaging data.

Usage

FSL version 6.0.7 is available on Picotte. You can load it using the modulefile:

module load fsl/6.0.7

Then you can run FSL commands, of which there are many. For example:

$ fslmaths.fsl

Usage: fslmaths [-dt <datatype>] <first_input> [operations and inputs] <output> [-odt <datatype>]

Datatype information:
 -dt sets the datatype used internally for calculations (default float for all except double images)
 -odt sets the output datatype (default as original image)
 Possible datatypes are: char short int float double
 Additionally "-dt input" will set the internal datatype to that of the original image

Binary operations:
  (some inputs can be either an image or a number)
 -add   : add following input to current image
 -sub   : subtract following input from current image
 -mul   : multiply current image by following input
 -div   : divide current image by following input
 -rem   : modulus remainder - divide current image by following input and take remainder
 -mas   : use (following image>0) to mask current image
 -thr   : use following number to threshold current image (zero anything below the number)\
 ...

Documentation

The FSL documentation is available online.